MAVEQC is a flexible R-package that provides QC analysis of Saturation Genome Editing (SGE) experimental data. Available under GPL 3.0 from https://github.com/wtsi-hgi/MAVEQC
Displays QC plots and statistics for all samples for QC.
Note: expected read length is 300, which is the sequencing length.
Note: the read length here is deducted by the length of primers, which assumes the reads in the input files have primers.(see 2.1. Sample Sheet: quants_append_start and quants_append_end)
Pass criterion: more than 90% of reads are longer than
200 nucleotides
Stats of missing variants in the library
Pass criterion: less than 1% of variants (library sequences) are missing
Note: Unique indicates that a template sequence occurs only once in the VaLiAnT meta file.This is important as a template sequence can occur more than once depending on the mutation types applied in VaLiAnT.
Displays the total number of reads per sample. Filtering based on 1-dimensional Kmean clustering that excludes unique sequences with low read counts.
Total Reads: the total number of raw reads
Note: No filtering happens in this step, only for clustering sequences (variants) based on read abundance
Displays the percentage of library reads vs non-library reads (ie. Reference, PAM and Unmapped) for Accepted Reads (see 2.2.3 explanation).
Pass criterion: more than 40% of accepted reads are
library reads
Defines the mean read count per template oligo sequence (dividing the total number of library reads by the total number of library sequences).
Pass criterion: library coverage is more than 100
Note: missing variants (0 count in the library) are not included.
Low Abundance cutoff: this cutoff is used to determine if the variant is
low abundance (the green dashed line in the figure)
% Low Abundance: the percentage of low-abundance variants
Pass criterion: the percentage of low-abundance variants is lower than 30%
Note: missing variants (0 count in the library) are not included.
condition_Day7_vs_Day4
condition_Day15_vs_Day4
condition_Day7_vs_Day4
condition_Day15_vs_Day4
Summarising the final results, below are the cutoffs using for PASS/FAIL